Everything below this point will be deleted by Friday Oct 23. If you have something recorded below that you want saved, please move information to the appropriate location above. All of the wiki links below should be under the DNA Protocols above as of now, but if anything is left out please contribute.

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==[[/Sequences|DNA Sequences]]==

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==Molecular protocols==

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===Labeling DNA for single-molecule stretching===

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Various methods to label dsDNA with digoxigenin (dig) and biotin for end-to-end stretching.

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* [[/Dig-bio PCR|PCR with labeled primers]]

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* klenow fill-in

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* ligating labeled duplexes (or hairpins)

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* ligating multiply-tagged segments.

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** (Useful for a couple of the above protocols): [[/Oligonucleotide Annealing|Oligo Annealing]]

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===Labeling DNA for unzipping===

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More complicated construction of a molecules that will unzip when stretched, as in our 2002 Biophys. J. paper PMID 12124289. Compared with DNA stretching, making a construct for unzipping presents many more potential pitfalls, and it is also challenging to get good yield.

* [[/Loading rate clamp|Loading rate clamp]]--method for stretching single-molecule tethers such that the force-versus-time curves are linear segments. Used in 2003 Phys. Rev. Let. paper, PMID 12906513, for unzipping with protein present, but can be used whenever the polymer physics are known ahead of time.

Current revision

One of the goals of our lab is to share protocols in a form that makes it as easy as possible for other labs to build off of them. These will be a combination of protocols that we will develop and also those that Steve has developed in the past but has not had a good opportunity to distribute yet. If any of the following protocols are of particular interest, drop us a line or make a note on the discussion page! We also want to share software applications and computational modules (mostly LabVIEW) that would be useful to others.